MolNFT v1 · #150349 · protein

KRAS-169 Q61H gppnhp + ch-2

6GQX · GTPase KRAS: “KRAS-169 Q61H gppnhp + ch-2”. X-ray diffraction, 3 ligands (GNP, F8K, MG), 12 pockets (best druggability 0.81). MolNFT v1 #150349 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6GQX
Type: protein
Length: 985 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GTPase KRAS
UniProt: P01116
Ligands: GNP, F8K, MG
Pockets: 12 · best druggability 0.81

Structure

x-ray diffraction · 6 distinct chains · 37% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	GTPase KRAS	protein	171	36% helix, 26% strand	P01116
B	GTPase KRAS	protein	169	36% helix, 26% strand	P01116
C	GTPase KRAS	protein	167	37% helix, 26% strand	P01116
D	GTPase KRAS	protein	158	37% helix, 26% strand	P01116
E	GTPase KRAS	protein	159	38% helix, 26% strand	P01116
F	GTPase KRAS	protein	161	38% helix, 26% strand	P01116

Ligands and binding sites

GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 6 copies · chains A, B, C, D, E, F
F8K · [4-[[2-methoxy-4-(3-methoxyphenyl) phenyl]amino]phenyl]methyl-dimethyl-azanium · ligand · 3 copies · chains A, C, B, E
MG · Magnesium ion · metal · 3 copies · chains A, B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	788	0.81	0.85	110	empty
2	1080	0.81	0.82	134	empty
3	138	0.61	0.85	28	MG, GNP
4	221	0.57	0.79	33	MG, GNP
5	138	0.56	0.83	30	MG, GNP

Interfaces

12 interfaces between chains.

A–C · 655 Å² buried · 9 hydrogen bonds · protein-protein
B–E · 599 Å² buried · 8 hydrogen bonds · protein-protein
D–F · 581 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 379 Å² buried · 8 hydrogen bonds · protein-protein
E–F · 367 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

6GQX · KRAS-169 Q61H gppnhp + ch-2 · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P01116
Elsewhere: RCSB PDB 6GQX · PDBe 6GQX · UniProt P01116

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